ABSTRACT Periodontitis affects about a third of the adult population, and it occurs in an aggressive form in approximately 1% of children. Its polymicrobial etiology is still incompletely understood. The oral microbiome consists of at least 600 species, and many of these have not yet been cultured in the laboratory. Recent, open-ended studies utilizing DNA-based methods have revealed a complex bacterial community structure, and new candidate species, many of them uncultivated, appear to be important in disease. Even for species with cultured representatives, the clonal laboratory isolates represent only a snapshot of the genomic diversity and physiological potential of the large number of lineages that represent that species in the heterogeneous human population. Our plan is to use large-scale small subunit ribosomal RNA (16S rRNA) analysis to determine the distribution and association of bacterial species in periodontitis as compared to periodontal health. We will conduct these studies in adults with recently active recurrent chronic periodontitis and children with newly diagnosed localized aggressive periodontitis, both as compared to matched, healthy individuals. We will then use this information to target uncultivated species and populations of bacteria specific to disease for metagenomic characterization, and to identify optimal human sources of samples for these studies. Since comprehensive genomic characterization of the oral microbiome by direct sequencing ("shotgun" metagenomics) is limited by the enormous microbial diversity and the uneven frequencies of the different organisms, we will use a novel approach, targeted metagenomics, to specifically separate and sequence the metagenomes of selected populations of uncultured bacteria from the oral microbiome. The proposed studies will provide a model approach to study uncultured subcomponents of the complex microbial communities that constitute the human microbiome by bridging the genomics of cultured, single lineage microbes with community shotgun metagenomics, This analysis will be integrated within a clinical and statistical framework, and will allow us to begin to elucidate the role of uncultivated members of the oral microbiome in human health and disease.